This page contains various information relating to vectors used in OpenWetWare labs.
Stringent vs. relaxed replication
Plasmid replication control is usually controlled by balancing the levels of a positive and a negative regulator of replication. For some plasmids (pMB1/colE1 replicons) the positive regulator is an RNA and in others (e.g. pSC101) it is a protein. Plasmids with a protein positive regulator will not replicate in the abscence of protein production - stringent control (although not the same as the stringent response due to a shortage of loaded tRNAs). Plasmids with an RNA positive regulator will continue to replicate in the abscence of protein production. This is termed relaxed control. High yields of plasmid may be obtained by halting protein production (via chloroamphenicol) when the culture reaches a high density and then continuing incubation for a number of hours. This might be of practical relevance when prepping the 1 and 3 series of Synthetic Biology plasmids.--BC 19:05, 3 Sep 2005 (EDT)
Online Vector Databases
VectorDB contains information about many common vectors, including yeast vectors.
The EMBL Hamburg outstation maintains a large database of vectors.
For eukaryotic vectors (Fish, Xenopus) see Minnesota.
The Forsburg Lab maintains a list of Fisson Yeast vectors.
Promega maintains a list of their vectors.
NEB maintains a list of common vectors.
Epicentre also maintains its own list.
Lucigen provides transcription-free vectors for cloning AT-rich and other difficult DNAs.
Addgene's Vector DB contains most of the information from Stanford's VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts. (However, it seems to be rather sparse when it comes to Escherichia coli vectors.) Note that Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. They encourage and invite labs to deposit plasmids at Addgene. They help you with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.
Bioinfoman also has a 5000+ long list of vector sequences.
PlasmID is an online database and DNA repository maintained for plasmids, including empty vectors useful for a variety of techniques, and open reading frame (ORF) clones relevant to human, yeast, and several bacterial pathogens. All clones can be requested individually, and ORF clones can also be viewed and requested as grouped collections. PlasmID is maintained by the DF/HCC DNA Resource Core at the Harvard Institute of Proteomics, Harvard Medical School.
PlasMapper: "automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format." It can also output GenBank format. Reference: Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart "PlasMapper: a web server for drawing and auto-annotating plasmid maps" Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.
- One drawback to this tool is that although it finds ORFs, it doesn't necessarily identify them. -- RS
- A very nice aspect of PlasMapper is that it identifies features of a sequence and puts them into GenBank format - very handy to prepare sequences for submission to GenBank. --User:Rgodiska
Also check out APe, A Plasmid Editor.
- Has some built-in features for annotation (a few genes, many restriction enzymes). Allows you to make custom "feature libraries" for annotating sequences
- Can edit features found, unlike Plasmapper --mel 18:50, 12 June 2007 (EDT)
- Novick RP, Clowes RC, Cohen SN, Curtiss R 3rd, Datta N, and Falkow S. Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev. 1976 Mar;40(1):168-89.